I need advice regarding the best tool for predicting transmembrane domain structure. I know transmembrane domain structures are a difficult niche. We have mutated a single position in a transmembrane domain that has produced a phenotype. We suspect the mutation is preventing binding with another protein within the transmembrane. We want to know the effect of the mutation on the structure of the protein's transmembrane domain.
I have experience with Modeller and SwissModel, however, this was over a year ago and I was wondering is there more appropriate or better tools for this job. Is it simply a matter of tool preference or is there a clear best practice tool?
The protein is highly conserved, with structures in the PDB, however the structures do NOT include the transmembrane domain.